{"id":16511311,"url":"https://github.com/pbenner/modhmm","last_synced_at":"2025-10-28T03:32:06.646Z","repository":{"id":57535510,"uuid":"147299032","full_name":"pbenner/modhmm","owner":"pbenner","description":"ModHMM Genome Segmentation Method","archived":false,"fork":false,"pushed_at":"2023-01-26T08:24:05.000Z","size":1298,"stargazers_count":4,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-01T11:24:30.617Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Go","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pbenner.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-09-04T06:34:28.000Z","updated_at":"2023-01-27T10:45:40.000Z","dependencies_parsed_at":"2023-02-14T15:15:43.606Z","dependency_job_id":null,"html_url":"https://github.com/pbenner/modhmm","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pbenner%2Fmodhmm","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pbenner%2Fmodhmm/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pbenner%2Fmodhmm/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pbenner%2Fmodhmm/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pbenner","download_url":"https://codeload.github.com/pbenner/modhmm/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238590596,"owners_count":19497350,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-11T15:59:47.439Z","updated_at":"2025-10-28T03:32:01.102Z","avatar_url":"https://github.com/pbenner.png","language":"Go","funding_links":[],"categories":[],"sub_categories":[],"readme":"## ModHMM\n\nModHMM is a genome segmentation method that is easy to apply and requires no manual interpretation of hidden states. It provides highly accurate annotations of chromatin states including active promoters and enhancers. The following is a list of states detected by ModHMM:\n\nState name | Description\n-----------|------------------------------------------\nPA         | active promoter\nEA         | active enhancer\nBI         | bivalent region\nPR         | primed region\nEA:tr      | active enhancer in a transcribed region\nBI:tr      | bivalet region in a transcribed region\nPR:tr      | primed region in a transcribed region\nTR         | transcribed region\nR1         | H3K27me3 repressed\nR2         | H3K9me3 repressed\nNS         | no signal\nCL         | control signal\n\nReferences:\n\nPhilipp Benner and Martin Vingron. *ModHMM: A Modular Supra-Bayesian Genome Segmentation Method*. Journal of Computational Biology. Apr 2020. 442-457. [[Link]](http://doi.org/10.1089/cmb.2019.0280)\n\n\u003ccenter\u003e\u003cimg src=\"https://raw.githubusercontent.com/pbenner/modhmm/master/README_example1.png\" alt=\"ModHMM\" width=\"720\" height=\"429\" /\u003e\u003c/center\u003e\n\n## Contact\n\nE-Mail: \u003cphilipp.benner@bäm.de\u003e (replace `ä` with `a`).\n\n### Available Segmentations\n\nModHMM segmentations are available for several ENCODE data sets:\n\nTissue | Version | Segmentation | Posteriors | Config | Comment\n-------|---------|--------------|------------|--------|--------\nGRCh38 ascending aorta | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-ascending-aorta/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/GRCh38-ascending-aorta/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-ascending-aorta.json) | total RNA-seq\nGRCh38 gastrocnemius medialis | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-gastrocnemius-medialis/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/GRCh38-gastrocnemius-medialis/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-gastrocnemius-medialis.json) | total RNA-seq\nGRCh38 heart left ventricle | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-heart-left-ventricle/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/GRCh38-heart-left-ventricle/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-heart-left-ventricle.json) | total RNA-seq\nGRCh38 lung upper lobe | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-lung-upper-lobe/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/GRCh38-lung-upper-lobe/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-lung-upper-lobe.json) | total RNA-seq\nGRCh38 pancreas body | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-pancreas-body/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/GRCh38-pancreas-body/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-pancreas-body.json) | total RNA-seq\nGRCh38 spleen | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-spleen/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/GRCh38-spleen/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-spleen.json) | total RNA-seq\nGRCh38 stomach | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-stomach/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/GRCh38-stomach/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-stomach.json) | total RNA-seq\nGRCh38 tibial nerve | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-tibial-nerve/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/GRCh38-tibial-nerve/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-tibial-nerve.json) | total RNA-seq\nGRCh38 transverse colon | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-transverse-colon/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/GRCh38-transverse-colon/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-transverse-colon.json) | total RNA-seq\nGRCh38 uterus | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-uterus/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/GRCh38-uterus/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/GRCh38-uterus.json) | total RNA-seq\nmm10 forebrain embryo day11.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day11.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-forebrain-embryo-day11.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day11.5.json) | poly-A RNA-seq\nmm10 forebrain embryo day12.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day12.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-forebrain-embryo-day12.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day12.5.json) | poly-A RNA-seq\nmm10 forebrain embryo day13.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day13.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-forebrain-embryo-day13.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day13.5.json) | poly-A RNA-seq\nmm10 forebrain embryo day14.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day14.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-forebrain-embryo-day14.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day14.5.json) | poly-A RNA-seq\nmm10 forebrain embryo day15.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day15.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-forebrain-embryo-day15.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day15.5.json) | poly-A RNA-seq\nmm10 forebrain embryo day16.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day16.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-forebrain-embryo-day16.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-forebrain-embryo-day16.5.json) | poly-A RNA-seq\nmm10 heart embryo day14.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-heart-embryo-day14.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-heart-embryo-day14.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-heart-embryo-day14.5.json) | poly-A RNA-seq\nmm10 heart embryo day15.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-heart-embryo-day15.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-heart-embryo-day15.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-heart-embryo-day15.5.json) | poly-A RNA-seq\nmm10 hindbrain embryo day11.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day11.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-hindbrain-embryo-day11.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day11.5.json) | poly-A RNA-seq\nmm10 hindbrain embryo day12.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day12.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-hindbrain-embryo-day12.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day12.5.json) | poly-A RNA-seq\nmm10 hindbrain embryo day13.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day13.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-hindbrain-embryo-day13.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day13.5.json) | poly-A RNA-seq\nmm10 hindbrain embryo day14.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day14.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-hindbrain-embryo-day14.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day14.5.json) | poly-A RNA-seq\nmm10 hindbrain embryo day15.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day15.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-hindbrain-embryo-day15.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day15.5.json) | poly-A RNA-seq\nmm10 hindbrain embryo day16.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day16.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-hindbrain-embryo-day16.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-hindbrain-embryo-day16.5.json) | poly-A RNA-seq\nmm10 kidney embryo day14.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-kidney-embryo-day14.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-kidney-embryo-day14.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-kidney-embryo-day14.5.json) | poly-A RNA-seq\nmm10 kidney embryo day15.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-kidney-embryo-day15.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-kidney-embryo-day15.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-kidney-embryo-day15.5.json) | poly-A RNA-seq\nmm10 kidney embryo day16.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-kidney-embryo-day16.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-kidney-embryo-day16.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-kidney-embryo-day16.5.json) | poly-A RNA-seq\nmm10 limb embryo day14.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-limb-embryo-day14.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-limb-embryo-day14.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-limb-embryo-day14.5.json) | poly-A RNA-seq\nmm10 limb embryo day15.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-limb-embryo-day15.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-limb-embryo-day15.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-limb-embryo-day15.5.json) | poly-A RNA-seq\nmm10 liver embryo day11.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day11.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-liver-embryo-day11.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day11.5.json) | poly-A RNA-seq\nmm10 liver embryo day12.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day12.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-liver-embryo-day12.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day12.5.json) | poly-A RNA-seq\nmm10 liver embryo day13.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day13.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-liver-embryo-day13.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day13.5.json) | poly-A RNA-seq\nmm10 liver embryo day14.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day14.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-liver-embryo-day14.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day14.5.json) | poly-A RNA-seq\nmm10 liver embryo day15.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day15.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-liver-embryo-day15.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day15.5.json) | poly-A RNA-seq\nmm10 liver embryo day16.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day16.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-liver-embryo-day16.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-liver-embryo-day16.5.json) | poly-A RNA-seq\nmm10 lung embryo day14.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-lung-embryo-day14.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-lung-embryo-day14.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-lung-embryo-day14.5.json) | poly-A RNA-seq\nmm10 lung embryo day15.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-lung-embryo-day15.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-lung-embryo-day15.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-lung-embryo-day15.5.json) | poly-A RNA-seq\nmm10 lung embryo day16.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-lung-embryo-day16.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-lung-embryo-day16.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-lung-embryo-day16.5.json) | poly-A RNA-seq\nmm10 midbrain embryo day11.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day11.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-midbrain-embryo-day11.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day11.5.json) | poly-A RNA-seq\nmm10 midbrain embryo day12.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day12.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-midbrain-embryo-day12.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day12.5.json) | poly-A RNA-seq\nmm10 midbrain embryo day13.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day13.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-midbrain-embryo-day13.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day13.5.json) | poly-A RNA-seq\nmm10 midbrain embryo day14.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day14.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-midbrain-embryo-day14.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day14.5.json) | poly-A RNA-seq\nmm10 midbrain embryo day15.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day15.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-midbrain-embryo-day15.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day15.5.json) | poly-A RNA-seq\nmm10 midbrain embryo day16.5 | 1.2.2 | [Segmentation](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day16.5/segmentation.bed.gz) |   [Posteriors](https://owww.molgen.mpg.de/~benner/pool/modhmm/mm10-midbrain-embryo-day16.5/) |       [Config](https://github.com/pbenner/modhmm-segmentations/raw/master/mm10-midbrain-embryo-day16.5.json) | poly-A RNA-seq\n\n### Installation\n\nModHMM can be installed by either downloading a binary from the [binary repository](https://github.com/pbenner/modhmm-binary) or by compiling the program from source.\n\nTo compile ModHMM you must first install the [Go compiler](https://golang.org/dl/). Afterwards, ModHMM can be installed as follows:\n```sh\n  go install -v github.com/pbenner/modhmm@latest\n```\n\nAlternatively, it is also possible to clone the repository and compile modhmm manually\n```sh\n  git clone github.com/pbenner/modhmm\n  make\n  make install\n```\n\n### Computing ModHMM Segmentations\n\nUnlike most other genome segmentation methods, ModHMM so far depends on data from a fixed set of features or assays (ATAC/DNase, H3K27ac, H3K9me3, H3K27me3, H3K4me1, H3K4me3, WCE/IgG, and RNA-seq). Open chromatin information must be either provided as ATAC-seq or DNase-seq data. Preferentially, the data should be given as BAM files, but it is also possible to use bigWig files as input.\n\nModHMM requires a configuration file in JSON format. The following is a simple example where data is provided as BAM files:\n```R\n{\n    # Directory containing feature alignment files\n    \"Bam Directory\" : \".bam\",\n    # Names of alignment files (for each feature a comma separated list of\n    # replicates must be specified, any number of replicates is supported)\n    \"Bam Files\"     : {\n        \"ATAC\"      : [    \"atac-rep1.bam\",     \"atac-rep2.bam\"],\n        #\"DNase\"    : [   \"dnase-rep1.bam\",    \"dnase-rep2.bam\"],\n        \"H3K27ac\"   : [ \"h3k27ac-rep1.bam\",  \"h3k27ac-rep2.bam\"],\n        \"H3K27me3\"  : [\"h3k27me3-rep1.bam\", \"h3k27me3-rep2.bam\"], # optional feature\n        \"H3K9me3\"   : [ \"h3k9me3-rep1.bam\",  \"h3k9me3-rep2.bam\"], # optional feature\n        \"H3K4me1\"   : [ \"h3k4me1-rep1.bam\",  \"h3k4me1-rep2.bam\"],\n        \"H3K4me3\"   : [ \"h3k4me3-rep1.bam\",  \"h3k4me3-rep2.bam\"],\n        \"RNA\"       : [     \"rna-rep1.bam\",      \"rna-rep2.bam\"],\n        \"Control\"   : [ \"control-rep1.bam\",  \"control-rep2.bam\"]  # optional feature\n    },\n    # Number of threads used for computing coverage bigWigs (memory intense!)\n    \"Coverage Threads\"                : 5,\n    # Directory containing all auxiliary files and the final segmentation\n    \"Directory\"                       : \"mm10-liver-embryo-day12.5\",\n    \"Description\"                     : \"liver embryo day12.5\",\n    # Number of threads used for evaluating classifiers and computing the segmentation\n    \"Threads\"                         : 20,\n    # Verbose level (0: no output, 1: low, 2: high)\n    \"Verbose\"                         : 1\n}\n```\nModHMM computes segmentations in several stages. At every stage the output is saved as a bigWig file, which can be inspected in a genome browser. The location and name of each bigWig file can be configured. A full set of all options is printed with `modhmm --genconf`.\n\nTo execute ModHMM simply run (assuming the configuration file is named `config.json`):\n```sh\n  modhmm -c config.json segmentation\n```\n\n### Extracting Promoter and Enhancer Predictions\n\nGenome segmentations are discretized predictions of chromatin states. They do not contain any information about the certainty of a particular prediction. Another drawback is that the number of predicted promoters and enhancers depends on the quality of the data, in particular the sequencing depth. Especially for differential analysis the dependency on the data quality might be hindering. In addition to genome segmentations, ModHMM can compute chromatin state probabilities:\n```sh\n  modhmm -c config.json eval-posterior-marginals\n```\nThis command will compute genome-wide probabilities for all chromatin states and export them as bigWig files named `posterior-marginal-STATE.bw`. By default, probabilities are on *log-scale*. With the option `--std-scale` ModHMM exports probabilities on standard scale. In this case, bigWig files are named `posterior-marginal-exp-STATE.bw`.\n\nModHMM also implements a simple peak-finding algorithm that can be used to call high-probability regions in chromatin state probability tracks:\n```sh\n  modhmm -c config.json call-posterior-marginal-peaks --threshold=0.8\n```\nThis command outputs tables with identified peaks, i.e. all regions with probabilities higher than the given threshold.\n\n### Using ModHMM as a Peak Caller\n\nMost peak callers use a single pre-defined model for computing enrichment probabilities and detecting peaks. In most cases there is a strong model misfit, because of the strong heterogeneity of ChIP-seq data. ModHMM instead allows to fit a mixture distribution (single-feature model) to the observed coverage values with a user-defined set of components. The following command calls ATAC-seq peaks using the estimated single-feature model, if available (see previous section):\n```sh\n  modhmm -c config.json call-single-feature-peaks atac\n```\n\n### Using bigWig files as input\nThe following configuration can be used if data instead is given in bigWig format:\n```R\n{\n    # Data is provided as bigWig files. Set all coverage files static!\n    \"Coverage Files\": {\n        \"ATAC\"   : {\"Filename\": \"coverage-atac.bw\",    \"Static\": true },\n        #\"DNase\" : {\"Filename\": \"coverage-dnase.bw\",   \"Static\": true },\n        \"H3K27ac\": {\"Filename\": \"coverage-h3k27ac.bw\", \"Static\": true },\n        \"H3K4me1\": {\"Filename\": \"coverage-h3k4me1.bw\", \"Static\": true },\n        \"H3K4me3\": {\"Filename\": \"coverage-h3k4me3.bw\", \"Static\": true },\n        \"RNA\"    : {\"Filename\": \"coverage-rna.bw\",     \"Static\": true },\n        \"Control\": {\"Filename\": \"coverage-control.bw\", \"Static\": true }\n    },\n    # Directory containing all auxiliary files and the final segmentation\n    \"Directory\"                       : \"mm10-liver-embryo-day12.5\",\n    \"Description\"                     : \"liver embryo day12.5\",\n    # Number of threads used for evaluating classifiers and computing the segmentation\n    \"Threads\"                         : 20,\n    # Verbose level (0: no output, 1: low, 2: high)\n    \"Verbose\"                         : 1\n}\n```\nCoverage bigWig files should contain discrete count data and must be placed in the directory `mm10-liver-embryo-day12.5`. Setting the option `Static` to true tells ModHMM that the provided bigWig files are not automatically generated and should not be overwritten.\n\n### Use Cases\n#### Example 1: Compute segmentation on ENCODE data from mouse embyonic liver at day 12.5\n\nCreate a configuration file named `mm10-liver-embryo-day12.5.json` (ModHMM accepts an extended JSON format that allows comments):\n```R\n{\n    \"Bam Directory\" : \".bam\",\n    \"Bam Files\"     : {\n        \"ATAC\"      : [\"ENCFF929LOH.bam\", \"ENCFF848NLJ.bam\"],\n        \"H3K27ac\"   : [\"ENCFF524ZFV.bam\", \"ENCFF322QGS.bam\"],\n        \"H3K27me3\"  : [\"ENCFF811DWT.bam\", \"ENCFF171KAM.bam\"],\n        \"H3K9me3\"   : [\"ENCFF293UCG.bam\", \"ENCFF777XFH.bam\"],\n        \"H3K4me1\"   : [\"ENCFF788JMC.bam\", \"ENCFF340ACH.bam\"],\n        \"H3K4me3\"   : [\"ENCFF211WGC.bam\", \"ENCFF587PZE.bam\"],\n        \"RNA\"       : [\"ENCFF405LEY.bam\", \"ENCFF627PCS.bam\"],\n        \"Control\"   : [\"ENCFF865QGZ.bam\", \"ENCFF438RYK.bam\"]\n    },\n    \"Coverage Threads\"                : 5,\n    \"Directory\"                       : \"mm10-liver-embryo-day12.5\",\n    \"Description\"                     : \"liver embryo day12.5\",\n    \"Threads\"                         : 20,\n    \"Verbose\"                         : 1\n}\n```\nENCODE bam files will be automatically downloaded by ModHMM.\n\nCreate output directory\n```sh\n  mkdir mm10-liver-embryo-day12.5\n```\n\nExecute ModHMM:\n```sh\n  modhmm -c mm10-liver-embryo-day12.5.json segmentation\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpbenner%2Fmodhmm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpbenner%2Fmodhmm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpbenner%2Fmodhmm/lists"}